[2024-01-25 18:15:35,536] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:35,537] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:35,538] [INFO] DQC Reference Directory: /var/lib/cwl/stge0fb7518-abca-4f08-a58a-b702d9a9d222/dqc_reference
[2024-01-25 18:15:36,662] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:36,663] [INFO] Task started: Prodigal
[2024-01-25 18:15:36,663] [INFO] Running command: gunzip -c /var/lib/cwl/stg164abc14-082c-420c-a6f8-2173eb698aef/GCF_027921905.1_ASM2792190v1_genomic.fna.gz | prodigal -d GCF_027921905.1_ASM2792190v1_genomic.fna/cds.fna -a GCF_027921905.1_ASM2792190v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:55,463] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:55,463] [INFO] Task started: HMMsearch
[2024-01-25 18:15:55,463] [INFO] Running command: hmmsearch --tblout GCF_027921905.1_ASM2792190v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0fb7518-abca-4f08-a58a-b702d9a9d222/dqc_reference/reference_markers.hmm GCF_027921905.1_ASM2792190v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:55,848] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:55,849] [INFO] Found 6/6 markers.
[2024-01-25 18:15:55,925] [INFO] Query marker FASTA was written to GCF_027921905.1_ASM2792190v1_genomic.fna/markers.fasta
[2024-01-25 18:15:55,926] [INFO] Task started: Blastn
[2024-01-25 18:15:55,928] [INFO] Running command: blastn -query GCF_027921905.1_ASM2792190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0fb7518-abca-4f08-a58a-b702d9a9d222/dqc_reference/reference_markers.fasta -out GCF_027921905.1_ASM2792190v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:57,243] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:57,246] [INFO] Selected 26 target genomes.
[2024-01-25 18:15:57,246] [INFO] Target genome list was writen to GCF_027921905.1_ASM2792190v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:57,304] [INFO] Task started: fastANI
[2024-01-25 18:15:57,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg164abc14-082c-420c-a6f8-2173eb698aef/GCF_027921905.1_ASM2792190v1_genomic.fna.gz --refList GCF_027921905.1_ASM2792190v1_genomic.fna/target_genomes.txt --output GCF_027921905.1_ASM2792190v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:49,198] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:49,199] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0fb7518-abca-4f08-a58a-b702d9a9d222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:49,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0fb7518-abca-4f08-a58a-b702d9a9d222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:49,216] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:16:49,216] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:49,216] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Streptomyces poonensis	strain=JCM 4815	GCA_014650915.1	68255	68255	type	True	99.992	2418	2435	95	conclusive
Streptomyces ruber	strain=JCM 3131	GCA_014648075.1	83378	83378	type	True	89.6902	1686	2435	95	below_threshold
Streptomyces phyllanthi	strain=TISTR 2346	GCA_009377205.1	1803180	1803180	type	True	85.989	1407	2435	95	below_threshold
Streptomyces spongiae	strain=NBRC 106415	GCA_009377185.1	565072	565072	type	True	85.7892	1395	2435	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	84.8869	1565	2435	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	84.8624	1612	2435	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	84.8302	1581	2435	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	84.7995	1597	2435	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.6943	1615	2435	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	84.5789	1617	2435	95	below_threshold
Streptomyces capitiformicae	strain=CGMCC 4.7403	GCA_014653855.1	2014920	2014920	type	True	84.5459	1566	2435	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	84.5308	1578	2435	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	84.5031	1576	2435	95	below_threshold
Streptomyces capitiformicae	strain=1H-SSA4	GCA_002214185.1	2014920	2014920	type	True	84.5009	1592	2435	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	84.4991	1583	2435	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	84.4629	1443	2435	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	84.4356	1557	2435	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	84.4257	1560	2435	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	84.3946	1397	2435	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	84.3329	1554	2435	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.3111	1458	2435	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	84.2042	1599	2435	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	84.1759	1619	2435	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	84.1222	1463	2435	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	84.0807	1509	2435	95	below_threshold
Streptomyces thermoviolaceus subsp. thermoviolaceus	strain=NBRC 13905	GCA_012034235.1	66860	1952	type	True	83.2794	1247	2435	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:49,217] [INFO] DFAST Taxonomy check result was written to GCF_027921905.1_ASM2792190v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:49,218] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:49,218] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:49,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0fb7518-abca-4f08-a58a-b702d9a9d222/dqc_reference/checkm_data
[2024-01-25 18:16:49,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:49,289] [INFO] Task started: CheckM
[2024-01-25 18:16:49,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027921905.1_ASM2792190v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027921905.1_ASM2792190v1_genomic.fna/checkm_input GCF_027921905.1_ASM2792190v1_genomic.fna/checkm_result
[2024-01-25 18:18:32,635] [INFO] Task succeeded: CheckM
[2024-01-25 18:18:32,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:18:32,658] [INFO] ===== Completeness check finished =====
[2024-01-25 18:18:32,659] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:18:32,660] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027921905.1_ASM2792190v1_genomic.fna/markers.fasta)
[2024-01-25 18:18:32,660] [INFO] Task started: Blastn
[2024-01-25 18:18:32,660] [INFO] Running command: blastn -query GCF_027921905.1_ASM2792190v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0fb7518-abca-4f08-a58a-b702d9a9d222/dqc_reference/reference_markers_gtdb.fasta -out GCF_027921905.1_ASM2792190v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:18:34,825] [INFO] Task succeeded: Blastn
[2024-01-25 18:18:34,830] [INFO] Selected 20 target genomes.
[2024-01-25 18:18:34,830] [INFO] Target genome list was writen to GCF_027921905.1_ASM2792190v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:18:34,854] [INFO] Task started: fastANI
[2024-01-25 18:18:34,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg164abc14-082c-420c-a6f8-2173eb698aef/GCF_027921905.1_ASM2792190v1_genomic.fna.gz --refList GCF_027921905.1_ASM2792190v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027921905.1_ASM2792190v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:19:15,808] [INFO] Task succeeded: fastANI
[2024-01-25 18:19:15,821] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:19:15,821] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_014650915.1	s__Streptomyces poonensis	99.992	2418	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_000719105.1	s__Streptomyces sclerotialus_B	92.1148	1871	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648075.1	s__Streptomyces ruber	89.6638	1689	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009377205.1	s__Streptomyces phyllanthi	86.0154	1404	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	84.9124	1604	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_009852415.1	s__Streptomyces sp009852415	84.7325	1615	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905845.1	s__Streptomyces sp001905845	84.6236	1603	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905725.1	s__Streptomyces sp001905725	84.6049	1593	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203535.1	s__Streptomyces griseostramineus	84.5631	1572	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.88	99.76	0.99	0.98	3	-
GCF_000317595.1	s__Streptomyces ipomoeae	84.5027	1481	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
GCF_014905555.1	s__Streptomyces sp014905555	84.4583	1503	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006782915.1	s__Streptomyces calvus	84.422	1562	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.66	99.31	0.97	0.96	5	-
GCF_001417775.1	s__Streptomyces sp001417775	84.4095	1475	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	84.4042	1592	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719285.1	s__Streptomyces bicolor	84.3951	1586	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001509795.1	s__Streptomyces sp001509795	84.3913	1451	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.33	98.67	0.96	0.93	3	-
GCF_003963535.1	s__Streptomyces cyaneochromogenes	84.1665	1621	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506575.1	s__Streptomyces mexicanus	83.9567	1440	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.95	96.19	0.87	0.78	3	-
GCF_014650035.1	s__Streptomyces lucensis	83.8898	1409	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507435.1	s__Streptomyces sp001507435	83.6101	1467	2435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.91	96.23	0.91	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:19:15,823] [INFO] GTDB search result was written to GCF_027921905.1_ASM2792190v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:19:15,823] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:19:15,827] [INFO] DFAST_QC result json was written to GCF_027921905.1_ASM2792190v1_genomic.fna/dqc_result.json
[2024-01-25 18:19:15,827] [INFO] DFAST_QC completed!
[2024-01-25 18:19:15,828] [INFO] Total running time: 0h3m40s